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Consistency in species name #23

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Rekyt opened this issue Nov 20, 2020 · 0 comments
Open

Consistency in species name #23

Rekyt opened this issue Nov 20, 2020 · 0 comments

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@Rekyt
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Rekyt commented Nov 20, 2020

I've been trying to download a species list, then getting the traits for the list automatically.
However, there is a naming inconsistency in species names between function that gets you the occurrence/ranges of species, and the functions that gets the trait data.

The former need the species name with an underscore, while the latter need the species name separated by a space:

library("BIEN")
#> Warning: le package 'BIEN' a été compilé avec la version R 4.0.3
#> Le chargement a nécessité le package : RPostgreSQL
#> Warning: le package 'RPostgreSQL' a été compilé avec la version R 4.0.3
#> Le chargement a nécessité le package : DBI
#> Warning: le package 'DBI' a été compilé avec la version R 4.0.3
#> Type vignette("BIEN") or vignette("BIEN_tutorial") to get started
#> 

# Ranges work with species names with underscores and without
# But always return species names *with* underscores
BIEN_ranges_load_species("Arnica_ovata")
#> class       : SpatialPolygonsDataFrame 
#> features    : 1 
#> extent      : -173.2246, -104.9879, 30.87895, 67.90291  (xmin, xmax, ymin, ymax)
#> crs         : +proj=longlat +datum=WGS84 +no_defs 
#> variables   : 1
#> names       :      species 
#> value       : Arnica_ovata
BIEN_ranges_load_species("Arnica ovata")
#> class       : SpatialPolygonsDataFrame 
#> features    : 1 
#> extent      : -173.2246, -104.9879, 30.87895, 67.90291  (xmin, xmax, ymin, ymax)
#> crs         : +proj=longlat +datum=WGS84 +no_defs 
#> variables   : 1
#> names       :      species 
#> value       : Arnica_ovata

# Trait functions need species *without* underscores
BIEN_trait_species("Arnica_ovata")
#> data frame with 0 columns and 0 rows
tibble::as_tibble(BIEN_trait_species("Arnica ovata"))
#> # A tibble: 4 x 13
#>   scrubbed_specie~ trait_name trait_value unit  method latitude longitude
#>   <chr>            <chr>      <chr>       <chr> <chr>     <dbl>     <dbl>
#> 1 Arnica ovata     seed mass  1.357       mg    data ~       NA        NA
#> 2 Arnica ovata     whole pla~ Herb        <NA>  Speci~       NA        NA
#> 3 Arnica ovata     seed mass  1.357       mg    data ~       NA        NA
#> 4 Arnica ovata     whole pla~ Herb        <NA>  Speci~       NA        NA
#> # ... with 6 more variables: elevation_m <int>, url_source <chr>,
#> #   project_pi <chr>, project_pi_contact <chr>, access <chr>, id <dbl>

Created on 2020-11-20 by the reprex package (v0.3.0)

Session info
devtools::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  French_France.1252          
#>  ctype    French_France.1252          
#>  tz       Europe/Berlin               
#>  date     2020-11-20                  
#> 
#> - Packages -------------------------------------------------------------------
#>  package     * version date       lib source        
#>  ape           5.4-1   2020-08-13 [1] CRAN (R 4.0.3)
#>  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.3)
#>  BIEN        * 1.2.4   2020-02-27 [1] CRAN (R 4.0.3)
#>  callr         3.5.1   2020-10-13 [1] CRAN (R 4.0.3)
#>  class         7.3-17  2020-04-26 [2] CRAN (R 4.0.2)
#>  classInt      0.4-3   2020-04-07 [1] CRAN (R 4.0.3)
#>  cli           2.1.0   2020-10-12 [1] CRAN (R 4.0.3)
#>  codetools     0.2-18  2020-11-04 [1] CRAN (R 4.0.3)
#>  crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.3)
#>  DBI         * 1.1.0   2019-12-15 [1] CRAN (R 4.0.3)
#>  desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.3)
#>  devtools      2.3.2   2020-09-18 [1] CRAN (R 4.0.3)
#>  digest        0.6.27  2020-10-24 [1] CRAN (R 4.0.3)
#>  doParallel    1.0.16  2020-10-16 [1] CRAN (R 4.0.3)
#>  dplyr         1.0.2   2020-08-18 [1] CRAN (R 4.0.3)
#>  e1071         1.7-4   2020-10-14 [1] CRAN (R 4.0.3)
#>  ellipsis      0.3.1   2020-05-15 [1] CRAN (R 4.0.3)
#>  evaluate      0.14    2019-05-28 [1] CRAN (R 4.0.3)
#>  fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.3)
#>  fasterize     1.0.3   2020-07-27 [1] CRAN (R 4.0.3)
#>  foreach       1.5.1   2020-10-15 [1] CRAN (R 4.0.3)
#>  fs            1.5.0   2020-07-31 [1] CRAN (R 4.0.3)
#>  generics      0.1.0   2020-10-31 [1] CRAN (R 4.0.3)
#>  glue          1.4.2   2020-08-27 [1] CRAN (R 4.0.3)
#>  highr         0.8     2019-03-20 [1] CRAN (R 4.0.3)
#>  htmltools     0.5.0   2020-06-16 [1] CRAN (R 4.0.3)
#>  iterators     1.0.13  2020-10-15 [1] CRAN (R 4.0.3)
#>  KernSmooth    2.23-18 2020-10-29 [1] CRAN (R 4.0.3)
#>  knitr         1.30    2020-09-22 [1] CRAN (R 4.0.3)
#>  lattice       0.20-41 2020-04-02 [2] CRAN (R 4.0.2)
#>  lifecycle     0.2.0   2020-03-06 [1] CRAN (R 4.0.3)
#>  magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.0.3)
#>  memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.3)
#>  nlme          3.1-150 2020-10-24 [1] CRAN (R 4.0.3)
#>  pillar        1.4.7   2020-11-20 [1] CRAN (R 4.0.2)
#>  pkgbuild      1.1.0   2020-07-13 [1] CRAN (R 4.0.3)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.0.3)
#>  pkgload       1.1.0   2020-05-29 [1] CRAN (R 4.0.3)
#>  prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.3)
#>  processx      3.4.4   2020-09-03 [1] CRAN (R 4.0.3)
#>  ps            1.4.0   2020-10-07 [1] CRAN (R 4.0.3)
#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.0.3)
#>  R6            2.5.0   2020-10-28 [1] CRAN (R 4.0.3)
#>  raster        3.3-13  2020-07-17 [1] CRAN (R 4.0.3)
#>  Rcpp          1.0.5   2020-07-06 [1] CRAN (R 4.0.3)
#>  remotes       2.2.0   2020-07-21 [1] CRAN (R 4.0.3)
#>  rgdal         1.5-18  2020-10-13 [1] CRAN (R 4.0.3)
#>  rgeos         0.5-5   2020-09-07 [1] CRAN (R 4.0.3)
#>  rlang         0.4.8   2020-10-08 [1] CRAN (R 4.0.3)
#>  rmarkdown     2.5     2020-10-21 [1] CRAN (R 4.0.3)
#>  RPostgreSQL * 0.6-2   2017-06-24 [1] CRAN (R 4.0.3)
#>  rprojroot     2.0.2   2020-11-15 [1] CRAN (R 4.0.2)
#>  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.3)
#>  sf            0.9-6   2020-09-13 [1] CRAN (R 4.0.3)
#>  sp            1.4-4   2020-10-07 [1] CRAN (R 4.0.3)
#>  stringi       1.5.3   2020-09-09 [1] CRAN (R 4.0.3)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.0.3)
#>  testthat      3.0.0   2020-10-31 [1] CRAN (R 4.0.3)
#>  tibble        3.0.4   2020-10-12 [1] CRAN (R 4.0.3)
#>  tidyselect    1.1.0   2020-05-11 [1] CRAN (R 4.0.3)
#>  units         0.6-7   2020-06-13 [1] CRAN (R 4.0.3)
#>  usethis       1.6.3   2020-09-17 [1] CRAN (R 4.0.3)
#>  utf8          1.1.4   2018-05-24 [1] CRAN (R 4.0.3)
#>  vctrs         0.3.4   2020-08-29 [1] CRAN (R 4.0.3)
#>  withr         2.3.0   2020-09-22 [1] CRAN (R 4.0.3)
#>  xfun          0.19    2020-10-30 [1] CRAN (R 4.0.3)
#>  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.0.3)
#> 
#> [1] C:/Users/ke76dimu/R/win-library/4.0
#> [2] C:/Program Files/R/R-4.0.2/library
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